add minimal testing

.gitignore

@@ -45,3 +45,5 @@ docs/_build
 
 # test harness
 test_harness.py
+
+apollo_shared_dir

.travis.yml

@@ -1,21 +1,39 @@
 language: python
+os: linux
+
 python:
-- '2.7'
-- '3.5'
-script:
-- pip install -U pip setuptools
-- pip install -U flake8
-- flake8 apollo --ignore=E501,W503 --exclude=arrow/commands/,scripts/
-- python setup.py install
-deploy:
-  provider: pypi
-  user: erasche
-  password:
-    secure: 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
-  on:
-    tags: true
-    distributions: sdist bdist_wheel
-    repo: galaxy-genome-annotation/python-apollo
+  - '2.7'
+  - '3.6'
+
+jobs:
+  include:
+    - stage: lint
+      install:
+        - pip install -U pip setuptools
+        - pip install -U flake8
+      script:
+        - flake8 apollo --ignore=E501,W503 --exclude=arrow/commands/,scripts/
+
+    - stage: test
+      install:
+        - pip install -U pip nose
+      script:
+        - python setup.py install
+        - export ARROW_GLOBAL_CONFIG_PATH=`pwd`/test-data/arrow.yml
+        - ./bootstrap_apollo.sh
+        - python setup.py nosetests
+
+    - stage: deploy
+      deploy:
+        provider: pypi
+        username: erasche
+        password:
+          secure: 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
+        on:
+          tags: true
+          distributions: "sdist bdist_wheel"
+          repo: galaxy-genome-annotation/python-apollo
+
 notifications:
   webhooks:
     urls:

README.rst

@@ -81,9 +81,10 @@ Or with the Arrow client:
 History
 -------
 
-- 3.2
+- 4.0
     - Added support for remote creation/update/deletion of organisms/tracks
     - Added support for adding GFF3 in the annotation track
+    - Added tests
 - 3.1
     - Added user activate/inactivate
     - Added get_creator for user, group and organisms

arrow/__init__.py

@@ -1 +1 @@
-__version__ = '3.1'
+__version__ = '4.0'

bootstrap_apollo.sh

@@ -0,0 +1,54 @@
+#!/bin/bash
+
+export GALAXY_SHARED_DIR=`pwd`/apollo_shared_dir
+mkdir -p "$GALAXY_SHARED_DIR"
+
+docker run -d -it -p 8888:8080 -v `pwd`/apollo_shared_dir/:`pwd`/apollo_shared_dir/ quay.io/gmod/apollo:2.4.1
+
+echo "[BOOTSTRAP] Waiting while Apollo starts up..."
+# Wait for apollo to be online
+for ((i=0;i<30;i++))
+do
+    APOLLO_UP=$(arrow users get_users 2> /dev/null | head -1 | grep '^\[$' -q; echo "$?")
+	if [[ $APOLLO_UP -eq 0 ]]; then
+		break
+	fi
+    sleep 10
+done
+
+if ! [[ $APOLLO_UP -eq 0 ]]; then
+    echo "Cannot connect to apollo for bootstrapping"
+    arrow users get_users
+    exit "${APOLLO_UP}"
+fi
+
+echo "[BOOTSTRAP] Apollo is up, bootstrapping for tests"
+
+# Create some groups
+arrow groups create_group one_group
+arrow groups create_group another_group
+
+# Create a user
+arrow users create_user "[email protected]" Junior Galaxy password
+
+# Add some organisms
+cp -r test-data/dataset_1_files/data/ "${GALAXY_SHARED_DIR}/org1"
+cp -r test-data/dataset_1_files/data/ "${GALAXY_SHARED_DIR}/org2"
+cp -r test-data/dataset_1_files/data/ "${GALAXY_SHARED_DIR}/org3"
+cp -r test-data/dataset_1_files/data/ "${GALAXY_SHARED_DIR}/org4"
+arrow organisms add_organism --genus Testus --species organus test_organism $GALAXY_SHARED_DIR/org1
+arrow organisms add_organism --genus Foo --species barus alt_org $GALAXY_SHARED_DIR/org2
+arrow organisms add_organism --genus Foo3 --species barus org3 $GALAXY_SHARED_DIR/org3
+arrow organisms add_organism --genus Foo4 --species barus org4 $GALAXY_SHARED_DIR/org4
+
+# Give access to organisms for test user
+arrow users update_organism_permissions --write --read --export "[email protected]" test_organism
+arrow users update_organism_permissions --write --read --export "[email protected]" alt_org
+arrow users update_organism_permissions --write --read --export "[email protected]" org3
+arrow users update_organism_permissions --write --read --export "[email protected]" org4
+
+# Load some annotations
+arrow annotations load_gff3 test_organism test-data/merlin.gff
+arrow annotations load_gff3 alt_org test-data/merlin.gff
+arrow annotations load_gff3 org3 test-data/merlin.gff
+arrow annotations load_gff3 org4 test-data/merlin.gff

setup.py

@@ -7,13 +7,16 @@
 except ImportError:
     from distutils.core import setup
 
+with open('requirements.txt') as f:
+    requires = f.read().splitlines()
+
 readme = open('README.rst').read()
 subpackages = [x.replace('/', '.') for x in glob.glob('arrow/commands/*') if not x.endswith('.py') and not x.endswith('.pyc')] + \
     [x.replace('/', '.') for x in glob.glob('apollo/*') if not x.endswith('.py') and not x.endswith('.pyc')] + ['arrow.commands']
 
 setup(
     name="apollo",
-    version='3.1',
+    version='4.0',
     description="Apollo API library",
     long_description=readme,
     author="Helena Rasche;Anthony Bretaudeau",
@@ -24,7 +27,7 @@
         [console_scripts]
         arrow=arrow.cli:arrow
     ''',
-    install_requires=['requests', 'biopython', 'cachetools', 'click>=6.7', 'wrapt', 'pyyaml', 'decorator', 'bcbio-gff'],
+    install_requires=requires,
     license="MIT",
     classifiers=[
         "Development Status :: 4 - Beta",

test-data/arrow.yml

@@ -0,0 +1,5 @@
+__default: local
+local:
+    url: "http://localhost:8888"
+    username: "[email protected]"
+    password: "password"

test-data/dataset_1.dat

@@ -0,0 +1,44 @@
+<!DOCTYPE html>
+<html>
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+    <title>JBrowse</title>
+
+    <link rel="apple-touch-icon" sizes="180x180" href="img/favicons/apple-touch-icon.png">
+    <link rel="icon" type="image/png" sizes="32x32" href="img/favicons/favicon-32x32.png">
+    <link rel="icon" type="image/png" sizes="16x16" href="img/favicons/favicon-16x16.png">
+    <link rel="manifest" href="site.webmanifest">
+    <link rel="mask-icon" href="img/favicons/safari-pinned-tab.svg" color="#5bbad5">
+    <meta name="msapplication-TileColor" content="#2d89ef">
+    <meta name="theme-color" content="#ffffff">
+
+    <script type="text/javascript">
+        window.onerror=function(msg){
+            if( document.body )
+                document.body.setAttribute("JSError",msg);
+        }
+        if(window.process&&process.versions&&process.versions.electron) {
+            window.electronRequire = require;
+            delete window.require;
+        }
+    </script>
+    <style>
+        html, body, div.jbrowse {
+            margin: 0;
+            padding: 0;
+            height: 100%;
+            width: 100%;
+        }
+    </style>
+    <script type="text/javascript" src="dist/main.bundle.js" charset="utf-8"></script>
+  </head>
+
+  <body>
+    <div class="jbrowse" id="GenomeBrowser" data-config='"allowCrossOriginDataRoot": false, "cacheBuster": true'>
+      <div id="LoadingScreen" style="padding: 50px;">
+        <h1>Loading...</h1>
+      </div>
+    </div>
+    <div style="display: none">JBrowseDefaultMainPage</div>
+  </body>
+</html>

test-data/dataset_1_files/data/.htaccess

@@ -0,0 +1,10 @@
+# This Apache .htaccess file is generated by JBrowse (GenomeDB) for
+# allowing cross-origin requests as defined by the Cross-Origin
+# Resource Sharing working draft from the W3C
+# (http://www.w3.org/TR/cors/).  In order for Apache to pay attention
+# to this, it must have mod_headers enabled, and its AllowOverride
+# configuration directive must allow FileInfo overrides.
+<IfModule mod_headers.c>
+    Header onsuccess set Access-Control-Allow-Origin *
+    Header onsuccess set Access-Control-Allow-Headers X-Requested-With,Range
+</IfModule>

test-data/dataset_1_files/data/names/02b/9.json

@@ -0,0 +1 @@
+{"merli":{"exact":[],"prefix":["Merlin"]}}

test-data/dataset_1_files/data/names/0e9/3.json

@@ -0,0 +1 @@
+{"mer":{"prefix":["Merlin"],"exact":[]}}

test-data/dataset_1_files/data/names/83f/8.json

@@ -0,0 +1 @@
+{"merlin":{"prefix":[],"exact":[["Merlin",null,"Merlin",null,0,172788,null]]}}

test-data/dataset_1_files/data/names/92c/2.json

@@ -0,0 +1 @@
+{"me":{"prefix":["Merlin"],"exact":[]}}

test-data/dataset_1_files/data/names/cf0/e.json

@@ -0,0 +1 @@
+{"merl":{"prefix":["Merlin"],"exact":[]}}

test-data/dataset_1_files/data/names/f26/8.json

@@ -0,0 +1 @@
+{"m":{"exact":[],"prefix":["Merlin"]}}

test-data/dataset_1_files/data/names/meta.json

@@ -0,0 +1 @@
+{"compress":0,"track_names":[],"format":"json","lowercase_keys":1,"hash_bits":16}